Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.50 kDa 
• Atom Count: 4765 
• Modelled Residue Count: 572 
• Deposited Residue Count: 650 
• Unique protein chains: 3

4BOH

Madanins (MEROPS I53) are cleaved by thrombin and factor Xa

• PDB DOI: 10.2210/pdb4BOH/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens, Haemaphysalis longicornis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-20 Released: 2013-09-04 
• Deposition Author(s): Figueiredo, A.C., deSanctis, D., Pereira, P.J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.239 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

The Tick-Derived Anticoagulant Madanin is Processed by Thrombin and Factor Xa.

Figueiredo, A.C., De Sanctis, D., Pereira, P.J.

(2013) PLoS One 8: 71866

• PubMed: 23951260 
• DOI: 10.1371/journal.pone.0071866
• Primary Citation of Related Structures:  
  4BOH


• PubMed Abstract: 
  

The cysteine-less peptidic anticoagulants madanin-1 and madanin-2 from the bush tick Haemaphysalis longicornis are the founding members of the MEROPS inhibitor family I53. It has been previously suggested that madanins exert their functional activity by competing with physiological substrates for binding to the positively charged exosite I (fibrinogen-binding exosite) of α-thrombin. We hereby demonstrate that competitive inhibition of α-thrombin by madanin-1 or madanin-2 involves binding to the enzyme's active site. Moreover, the blood coagulation factors IIa and Xa are shown to hydrolyze both inhibitors at different, although partially overlapping cleavage sites. Finally, the three-dimensional structure of the complex formed between human α-thrombin and a proteolytic fragment of madanin-1, determined by X-ray crystallography, elucidates the molecular details of madanin-1 recognition and processing by the proteinase. Taken together, the current findings establish the mechanism of action of madanins, natural anticoagulants that behave as cleavable competitive inhibitors of thrombin.

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Organizational Affiliation: 

IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN HEAVY CHAIN	A, C [auth H]	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN LIGHT CHAIN	B, D [auth L]	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN INHIBITOR MADANIN 1	E [auth M]	60	Haemaphysalis longicornis	Mutation(s): 0
UniProt
Find proteins for Q86FP9 (Haemaphysalis longicornis) Explore Q86FP9  Go to UniProtKB:  Q86FP9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], K [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	H [auth A], I [auth A], J [auth A], M [auth H], N [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	G [auth A], L [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.239 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.071	α = 90
b = 78.578	β = 90
c = 155.156	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-20 
• Released Date: 2013-09-04 
Deposition Author(s): Figueiredo, A.C., deSanctis, D., Pereira, P.J.B.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary